Hi Carl,
wrong mixing start: Flair 3 (from flair.cern) is being developed to be used with FLUKA v4 (from fluka.cern) and, as a matter of fact, cannot assure compatibility with other versions independently handled.
Indeed Flair takes the fluka executable in the bin subdirectory of the selected installation directory (not flukahp, which is not there).
This is a bug that will be fixed: as your experience suggests, one may want to set there (the full path of) a custom executable.
On the other hand, as you have likely realized already, you can pick up the latter in the Run tab.
Thanks